Sunday, January 17, 2016

A Textbook Example

The recent finding that the DNA packaging technology and structure, known as chromatin, is not limited to eukaryotes but is also present in archaea, and so from an evolutionary perspective must have “evolved before archaea and eukaryotes split apart—more than 2 billion years ago,” is merely the latest in a string of misadventures evolutionists have incurred ever since they stole the histones.

Histones are the hub-like proteins which (usually) serve as the hubs about which DNA is wrapped in the chromatin structure. Like a thread wrapped around a spool this design packs DNA away for storage with an incredible packing factor. Interestingly, the histone proteins are highly similar across vastly different species. Again, from an evolutionary perspective, this means they must have evolved early in evolutionary history to a very specific design. As one textbook explains:

The amino acid sequences of four histones (H2A, H2B, H3, and H4) are remarkably similar among distantly related species. For example, the sequences of histone H3 from sea urchin tissue and of H3 from calf thymus are identical except for a single amino acid, and only four amino acids are different in H3 from the garden pea and that from calf thymus. … The similarity in sequence among histones from all eukaryotes indicates that they fold into very similar three-dimensional conformations, which were optimized for histone function early in evolution in a common ancestor of all modern eukaryotes. [1]

But the new finding pushes back this evolutionary “optimization” far earlier in time. Once again, evolution’s heroics are moved to the distant past where no one can see. Early life was not simple.

And of course DNA needs to be accessed so this histone packaging is quite dynamic. It can roll or it can be removed and moved. The histones themselves have tails that stick out and are tagged with small chemical groups that influence whether the packaging is tight or unrolled. Again, early life was not simple.

But the fact that histones are so similar across a wide range of species leads to an entirely different dilemma for evolution. For from an evolutionary perspective, it means that the histones must not tolerate change very well. Here is how a leading 1994 textbook described it:

When the number of amino acid differences in a particular protein is plotted for several pairs of species against the time since the species diverged, the result is a reasonably straight line. That is, the longer the period since divergence, the larger the number of differences. … When various proteins are compared, each shows a different but characteristic rate of evolution. Since all DNA base pairs are thought to be subject to roughly the same rate of random mutation, these different rates must reflect differences in the probability that an organism with a random mutation over the given protein will survive and propagate. Changes in amino acid sequence are evidently much more harmful for some proteins than for others. From Table 6-2 we can estimate that about 6 of every 7 random amino acid changes are harmful over the long term in hemoglobin, about 29 of every 30 amino acid changes are harmful in cytochrome c, and virtually all amino acid changes are harmful in histone H4. We assume that individuals who carried such harmful mutations have been eliminated from the population by natural selection. [2]

So the reason the histone proteins are so similar, again from an evolutionary perspective, is because mutations changing those proteins could not be tolerated. This is the evolutionary prediction and here is how the next edition of that same textbook, eight years later in the year 2002, added to the discussion of the high similarity of the histone proteins:

As might be expected from their fundamental role in DNA packaging, the histones are among the most highly conserved eucaryotic proteins. For example, the amino acid sequence of histone H4 from a pea and a cow differ at only at 2 of the 102 positions. This strong evolutionary conservation suggests that the functions of histones involve nearly all of their amino acids, so that a change in any position is deleterious to the cell. This suggestion has been tested directly in yeast cells, in which it is possible to mutate a given histone gene in vitro and introduce it into the yeast genome in place of the normal gene. As might be expected, most changes in histone sequences are lethal; the few that are not lethal cause changes in the normal pattern of gene expression, as well as other abnormalities.

There was only one problem. That is false. In fact, even at the time studies had already shown that histone H4 could well tolerate many changes. It was not merely an example of evolution pointing in the wrong direction and producing yet another failed prediction. It was an all too frequent example of evolution abusing science, force-fitting results into its framework. And of course all of this became doctrine for wider consumption. As a 2001 PBS documentary stated:

Histones interact with DNA in the chromosomes, providing structural support and regulating DNA activities such as replication and RNA synthesis. Their ability to bind to DNA depends upon a particular structure and shape. Virtually all mutations impair histone's function, so almost none get through the filter of natural selection. The 103 amino acids in this protein are identical for nearly all plants and animals.

But it is not, and was not, true that “virtually all mutations impair histone’s function.” That was not science, it was dogma disguised as science. And since then the dogma has become even more obvious. As one recent paper summarized:

Furthermore, recent systematic mutagenesis studies demonstrate that, despite the extremely well conserved nature of histone residues throughout different organisms, only a few mutations on the individual residues (including nonmodiﬁable sites) bring about prominent phenotypic defects.

It is remarkable how many residues in these highly conserved proteins can be mutated and retain basic nucleosomal function. … The high level of sequence conservation of histone proteins across phyla suggests a fitness advantage of these particular amino acid sequences during evolution. Yet comprehensive analysis indicates that many histone mutations have no recognized phenotype.

In fact, even more surprising for evolutionists, many mutations actually raised the fitness level:

Surprisingly, a subset of 27 histone mutants show a higher intensity after growth (log2 ratio >+1.5) suggesting they are collectively fitter and maintain a selective advantage under glucose limitation.

It was yet another falsified evolutionary prediction, and yet another example of evolution abusing science.

Now evolutionists propose a redundancy hypothesis. Those histone mutations are well tolerated because evolution constructed a backup mechanism. Both mechanisms would have to mutate and fail before any lethal effects could be felt.

As usual, contradictory results are accommodated by patching the theory with yet more epicycles. The epicycles make the theory far more complex, and far more unlikely, if that were so possible. In this case, evolution not only struck on incredible complexity, and did so early in history (before there were eukaryotes and nucleus’s in which to pack the DNA), but the whole design now must have incorporated layers of redundancy which we haven’t even been able to figure out yet.

And all of this, evolutionists insist, must be a fact. Anyone who would so much as doubt this truth must be blackballed.

It has been one misstep after another ever since the evolutionists stole the histones. Evolution is truly a profound theory, not for what it reveals about nature, but for what it reveals about people. Religion drives science, and it matters.